====== VEP ======

**VEP** is a software module available on **Comet**.

===== VEP overview =====

To access **VEP** on Comet, run ''module load VEP''. This will load the //default// version of **VEP**.

An overview of the module information is shown below (''module -r spider ^VEP$''):

<code lang=text>
  VEP: VEP/113.3-GCC-13.3.0
    Description:
      Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on
      genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled
      replacements for frequently used routines in VEP.

    This module can be loaded directly: module load VEP/113.3-GCC-13.3.0

    This module provides the following extensions:

       Bio::EnsEMBL::XS/2.3.2 (E)

    Help:
      
      Description
      ===========
      Variant Effect Predictor (VEP) determines the effect of your
       variants (SNPs, insertions, deletions, CNVs or structural variants) on genes,
       transcripts, and protein sequence, as well as regulatory regions.
       Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
       used routines in VEP.
      
      More information
      ================
       - Homepage: https://www.ensembl.org/info/docs/tools/vep
      
      Included extensions
      ===================
      Bio::EnsEMBL::XS-2.3.2
</code>

If there are multiple versions of **VEP** listed, then you can load a //specific// version as follows:
<code lang=bash>
$ module load VEP/version_string
</code>

You can find the most //up to date information// whilst logged on to Comet by running ''module -r spider ^VEP$''.

----

===== VEP Help =====

The module **VEP** has the following embedded help text (''module help VEP''):

<code lang=text>Description
===========
Variant Effect Predictor (VEP) determines the effect of your
 variants (SNPs, insertions, deletions, CNVs or structural variants) on genes,
 transcripts, and protein sequence, as well as regulatory regions.
 Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
 used routines in VEP.

More information
================
 - Homepage: https://www.ensembl.org/info/docs/tools/vep

Included extensions
===================
Bio::EnsEMBL::XS-2.3.2

</code>

----

===== VEP Dependencies =====

The //default// version of the module **VEP** has the following dependencies:

   * GCC/13.3.0
   * Perl/5.38.2-GCCcore-13.3.0
   * Archive-Zip/1.68-GCCcore-13.3.0
   * DBD-mysql/4.051-GCC-13.3.0
   * BioPerl/1.7.8-GCCcore-13.3.0
   * Bio-DB-HTS/3.01-GCC-13.3.0
   * Compress-Raw-Zlib/2.213-GCCcore-13.3.0

----

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